Lab16_JohnBauer

library(tidyverse)

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library(knitr)
library(ggtree)

## ggtree v3.10.1 For help: https://yulab-smu.top/treedata-book/
## 
## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
## 
## Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
## ggtree: an R package for visualization and annotation of phylogenetic
## trees with their covariates and other associated data. Methods in
## Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
## 
## Guangchuang Yu. Using ggtree to visualize data on tree-like structures.
## Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
## 
## Guangchuang Yu.  Data Integration, Manipulation and Visualization of
## Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
## doi:10.1201/9781003279242
## 
## Attaching package: 'ggtree'
## 
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##     expand

library(TDbook) #A Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).
library(ggimage)
library(rphylopic)

## You are using rphylopic v.1.4.0. Please remember to credit PhyloPic contributors (hint: `get_attribution()`) and cite rphylopic in your work (hint: `citation("rphylopic")`).
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library(treeio)

## treeio v1.26.0 For help: https://yulab-smu.top/treedata-book/
## 
## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
## 
## LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
## Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
## for phylogenetic tree input and output with richly annotated and
## associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.
## doi: 10.1093/molbev/msz240
## 
## Guangchuang Yu.  Data Integration, Manipulation and Visualization of
## Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
## doi:10.1201/9781003279242
## 
## Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
## Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
## object for visualization of a phylogenetic tree and annotation data.
## iMeta 2022, 1(4):e56. doi:10.1002/imt2.56

library(tidytree)

## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
## 
## G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
## Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574
## 
## S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
## Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
## visualization of richly annotated phylogenetic data. Molecular Biology
## and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
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library(ape)

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library(TreeTools)

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library(phytools)

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library(ggnewscale)
library(ggtreeExtra)

## ggtreeExtra v1.12.0 For help: https://yulab-smu.top/treedata-book/
## 
## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
## 
## S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
## Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
## visualization of richly annotated phylogenetic data. Molecular Biology
## and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166

library(ggstar)
#library(ggeasy) #https://jonocarroll.github.io/ggeasy/
#library(DT)

NEON_MAGs <- read_csv("data/NEON/GOLD_Study_ID_Gs0161344_NEON_2024_4_21.csv") %>% 
  # remove columns that are not needed for data analysis
  select(-c(`GOLD Study ID`, `Bin Methods`, `Created By`, `Date Added`, `Bin Lineage`)) %>% 
  # create a new column with the Assembly Type
  mutate("Assembly Type" = case_when(`Genome Name` == "NEON combined assembly" ~ `Genome Name`,
                            TRUE ~ "Individual")) %>% 
  mutate_at("Assembly Type", str_replace, "NEON combined assembly", "Combined") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "d__", "") %>%  
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "p__", "") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "c__", "") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "o__", "") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "f__", "") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "g__", "") %>% 
  mutate_at("GTDB-Tk Taxonomy Lineage", str_replace, "s__", "") %>%
  separate(`GTDB-Tk Taxonomy Lineage`, c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species"), ";", remove = FALSE) %>% 
  mutate_at("Domain", na_if,"") %>% 
  mutate_at("Phylum", na_if,"") %>% 
  mutate_at("Class", na_if,"") %>% 
  mutate_at("Order", na_if,"") %>% 
  mutate_at("Family", na_if,"") %>% 
  mutate_at("Genus", na_if,"") %>% 
  mutate_at("Species", na_if,"") %>% 
  
  # Get rid of the the common string "Soil microbial communities from "
  mutate_at("Genome Name", str_replace, "Terrestrial soil microbial communities from ", "") %>% 
  # Use the first `-` to split the column in two
  separate(`Genome Name`, c("Site","Sample Name"), " - ") %>% 
  # Get rid of the the common string "S-comp-1"
  mutate_at("Sample Name", str_replace, "-comp-1", "") %>%
  # separate the Sample Name into Site ID and plot info
  separate(`Sample Name`, c("Site ID","subplot.layer.date"), "_", remove = FALSE,) %>% 
  # separate the plot info into 3 columns
  separate(`subplot.layer.date`, c("Subplot", "Layer", "Date"), "-") 

NEON_metagenomes <- read_tsv("data/NEON/exported_img_data_Gs0161344_NEON.tsv") %>% 
  select(-c(`Domain`, `Sequencing Status`, `Sequencing Center`)) %>% 
  rename(`Genome Name` = `Genome Name / Sample Name`) %>% 
  filter(str_detect(`Genome Name`, 're-annotation', negate = T)) %>% 
  filter(str_detect(`Genome Name`, 'WREF plot', negate = T)) 

NEON_metagenomes <- NEON_metagenomes %>% 
  # Get rid of the the common string "Soil microbial communities from "
  mutate_at("Genome Name", str_replace, "Terrestrial soil microbial communities from ", "") %>% 
  # Use the first `-` to split the column in two
  separate(`Genome Name`, c("Site","Sample Name"), " - ") %>% 
  # Get rid of the the common string "-comp-1"
  mutate_at("Sample Name", str_replace, "-comp-1", "") %>%
  # separate the Sample Name into Site ID and plot info
  separate(`Sample Name`, c("Site ID","subplot.layer.date"), "_", remove = FALSE,) %>% 
  # separate the plot info into 3 columns
  separate(`subplot.layer.date`, c("Subplot", "Layer", "Date"), "-")

NEON_chemistry <- read_tsv("data/NEON/neon_plot_soilChem1_metadata.tsv") %>% 
  # remove -COMP from genomicsSampleID
  mutate_at("genomicsSampleID", str_replace, "-COMP", "") 

NEON_MAGs_metagenomes_chemistry <- NEON_MAGs %>% 
  left_join(NEON_metagenomes, by = "Sample Name") %>% 
  left_join(NEON_chemistry, by = c("Sample Name" = "genomicsSampleID")) %>%
  rename("label" = "Bin ID")

tree_arc <- read.tree("data/NEON/gtdbtk.ar53.decorated.tree")
tree_bac <- read.tree("data/NEON/gtdbtk.bac120.decorated.tree")

#Gammaproteobacteria
NEON_MAGs_metagenomes_chemistry_Gammaproteobacteria <- NEON_MAGs_metagenomes_chemistry %>%
  filter(str_detect(`Class`,"Gammaproteobacteria"))

#Novel
NEON_MAGs_metagenomes_chemistry_Gammaproteobacteria_Novel <- NEON_MAGs_metagenomes_chemistry_Gammaproteobacteria %>%
  filter(is.na(Order) | is.na(Family) | is.na(Genus) | is.na(Species))
#almost are novel only two have species names


#Toolik
NEON_MAGs_metagenomes_chemistry_TOOL<- NEON_MAGs_metagenomes_chemistry %>% 
  filter(`Site ID.x` == "TOOL") %>% 
  filter(Domain == "Bacteria")
TOOL_MAGs_label <- NEON_MAGs_metagenomes_chemistry_TOOL$label
tree_bac_TOOL_MAGs <-drop.tip(tree_bac,tree_bac$tip.label[-match(TOOL_MAGs_label, tree_bac$tip.label)])

# Make a vector with the internal node lables
node_vector_bac = c(tree_bac$tip.label,tree_bac$node.label)

# Search for your Phylum or Class
grep("Gammaproteobacteria", node_vector_bac, value = TRUE)

## [1] "'1.0:c__Gammaproteobacteria'"

match(grep("Gammaproteobacteria", node_vector_bac, value = TRUE), node_vector_bac)

## [1] 3048

grep("Alphaproteobacteria", node_vector_bac, value = TRUE)

## [1] "'1.0:c__Alphaproteobacteria'"

match(grep("Alphaproteobacteria", node_vector_bac, value = TRUE), node_vector_bac)

## [1] 3171

grep("Pseudomonadota", node_vector_bac, value = TRUE)

## [1] "'1.0:p__Pseudomonadota'"

match(grep("Pseudomonadota", node_vector_bac, value = TRUE), node_vector_bac)

## [1] 3047

tree_bac_node_Gammaproteobacteria <- Preorder(tree_bac)
tree_Gammaproteobacteria <- Subtree(tree_bac_node_Gammaproteobacteria, 3048)

# Make a vector with the internal node lables
node_vector_bac_TOOL_MAGS = c(tree_bac_TOOL_MAGs$tip.label,tree_bac_TOOL_MAGs$node.label)

grep("Gammaproteobacteria", node_vector_bac_TOOL_MAGS, value = TRUE)

## [1] "'1.0:c__Gammaproteobacteria'"

match(grep("Gammaproteobacteria", node_vector_bac_TOOL_MAGS, value = TRUE), node_vector_bac_TOOL_MAGS)

## [1] 259

grep("Pseudomonadota", node_vector_bac_TOOL_MAGS, value = TRUE)

## [1] "'1.0:p__Pseudomonadota'"

match(grep("Pseudomonadota", node_vector_bac_TOOL_MAGS, value = TRUE), node_vector_bac_TOOL_MAGS)

## [1] 258

Trees

Gammmaproteobacteria Rectangular Tree

ggtree(tree_Gammaproteobacteria) +
  geom_tiplab(size=3) +
  xlim(0,20)

ggsave(
  "Gammmaproteobacteria_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria Circular Tree

ggtree(tree_Gammaproteobacteria, layout="circular") + 
  geom_tiplab(aes(angle=angle))+
    theme_tree() +
    xlim(0,20)

ggsave(
  "Gammmaproteobacteria_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

NEON MAGS Gammaproteobacteria Highlight Circular Tree

ggtree(tree_bac, layout="circular") +
    geom_hilight(node=3048, fill="steelblue", alpha=.6)

ggsave(
  "NEON_MAGS_Gammaproteobacteria_Highlight_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

NEON MAGS Gammaproteobacteria Highlight with Label Circular Tree

ggtree(tree_bac, layout="circular", branch.length="none") +
    geom_hilight(node=3047, fill="grey", alpha=.6) +
    geom_cladelab(node=3047, label="Pseudomonadota", align=TRUE, angle='auto', 
                  offset.text=0.5 , textcolor='black', barcolor='grey',barsize=1.5, fontsize=5)+
    geom_hilight(node=3048, fill="steelblue", alpha=.6) +
    geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE, angle='auto', offset=1,  
                  offset.text=0.5 , textcolor='black', barcolor='steelblue',barsize=1.5, fontsize=5)

ggsave(
  "NEON_MAGS_Gammaproteobacteria_Highlight_with_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 14 in image

NEON MAGS Gammaproteobacteria Label Circular Tree

ggtree(tree_bac, layout="circular", branch.length="none") %>% 
  collapse(node=3048) + 
  geom_point2(aes(subset=(node==3048)), shape=23, size=5, fill='steelblue') +  
  geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE,  
                  offset = 2, textcolor='steelblue')

ggsave(
  "NEON_MAGS_Gammaproteobacteria_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

NEON MAGS Gammaproteobacteria Minimized Circular Tree

p <- ggtree(tree_bac, layout="circular", branch.length="none")
scaleClade(p, 3048, .2) %>% collapse(3048, 'min', fill="steelblue")  +
  geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE,  
                  offset = 0.2, textcolor='steelblue')

ggsave(
  "NEON_MAGS_Gammaproteobacteria_Minimized_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Order Labels Circular Tree

ggtree(tree_Gammaproteobacteria, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  xlim(0,20) +
  geom_point(mapping=aes(color=Order))

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Order_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Order and Assembly Type Labels Circular Tree

ggtree(tree_Gammaproteobacteria, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  xlim(0,20) +
  geom_point(mapping=aes(color=Order, shape = `Assembly Type`)) 

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point()`).

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Order_and_Assembly_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point()`).

Gammaproteobacteria with Ecosystem Subtype System Rectangular Tree

ggtree(tree_Gammaproteobacteria)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  xlim(0,20) +
  geom_point(mapping=aes(color=`Ecosystem Subtype`))

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_System_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Site Location Rectangular Tree

ggtree(tree_Gammaproteobacteria)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  xlim(0,20) +
  geom_point(mapping=aes(color=`Site.y`)) +labs(color="Site")

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Site_Location_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Bin Completeness Label Rectangular Tree

ggtree(tree_Gammaproteobacteria)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Bin Completeness`)) + 
  scale_colour_gradient(low='blue', high='red') +
  geom_tiplab(size=2, hjust=-.1) +
  xlim(0,20)

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Bin_Completeness_Label_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Ecosystem Subtype and Total number of Bases Label Circular Tree

ggtree(tree_Gammaproteobacteria, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`))

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_and_Total_Number_of_Bases_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

Gammaproteobacteria triplot with Bin Completeness and Bin Contamination

# For unknown reasons the following does not like blank spaces in the names
NEON_MAGs_metagenomes_chemistry_noblank <- NEON_MAGs_metagenomes_chemistry %>% 
  rename("AssemblyType" = "Assembly Type") %>% 
  rename("BinCompleteness" = "Bin Completeness") %>% 
  rename("BinContamination" = "Bin Contamination") %>% 
  rename("TotalNumberofBases" = "Total Number of Bases") %>% 
  rename("EcosystemSubtype" = "Ecosystem Subtype") %>%
  rename("GeneCount" = "Gene Count") %>% 
  rename("GCassembled" = "GC  * assembled")

ggtree(tree_Gammaproteobacteria)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Ecosystem Subtype`)) + 

# For unknown reasons the following does not like blank spaces in the names
  geom_facet(panel = "Bin Completeness", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point, 
      mapping=aes(x = BinCompleteness)) +
  geom_facet(panel = "Bin Contamination", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col, 
                aes(x = BinContamination), orientation = 'y', width = .6) +
  theme_tree2(legend.position=c(.1, .7))

ggsave(
  "NEON_MAGS_Gammaproteobacteria_triplot_with_Bin_Completeness_and_Bin_Contamination.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria triplot with Gene and GC Content

ggtree(tree_Gammaproteobacteria)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Ecosystem Subtype`)) + 

# For unknown reasons the following does not like blank spaces in the names
  geom_facet(panel = "Gene Count", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point, 
      mapping=aes(x = GeneCount))+
  geom_facet(panel = "% GC Content ", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col, 
                aes(x = GCassembled), orientation = 'y', width = .6) +
  theme_tree2(legend.position=c(.1, .7))

ggsave(
  "NEON_MAGS_Gammaproteobacteria_triplot_with_ Gene_and_GC_Content.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Gammaproteobacteria with Ecosystem Subtype and Total Number of Bases in Outside Labels

ggtree(tree_Gammaproteobacteria, layout="circular", branch.length="none") %<+% 
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) + 
  new_scale_fill() + 
  geom_fruit(
      data=NEON_MAGs_metagenomes_chemistry_noblank,
      geom=geom_tile,
      mapping=aes(y=label, x=1, fill= AssemblyType),
      offset=0.08,   # The distance between external layers, default is 0.03 times of x range of tree.
      pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
      )

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_and_Total_Number_of_Bases_in_Outside_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

NEON with Ecosystem Subtype, Total Number of Bases, and Assembly type Outside Layer Label

ggtree(tree_bac, layout="circular", branch.length="none") %<+% 
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) + 
  new_scale_fill() + 
  geom_fruit(
      data=NEON_MAGs_metagenomes_chemistry_noblank,
      geom=geom_tile,
      mapping=aes(y=label, x=1, fill= AssemblyType),
      offset=0.08,   # The distance between external layers, default is 0.03 times of x range of tree.
      pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
      ) + 
  new_scale_fill() +
  geom_fruit(
          data=NEON_MAGs_metagenomes_chemistry_noblank,
          geom=geom_col,
          mapping=aes(y=label, x=TotalNumberofBases),  
          pwidth=0.4,
          axis.params=list(
                          axis="x", # add axis text of the layer.
                          text.angle=-45, # the text size of axis.
                          hjust=0  # adjust the horizontal position of text of axis.
                      ),
          grid.params=list() # add the grid line of the external bar plot.
      ) + 
      theme(#legend.position=c(0.96, 0.5), # the position of legend.
          legend.background=element_rect(fill=NA), # the background of legend.
          legend.title=element_text(size=7), # the title size of legend.
          legend.text=element_text(size=6), # the text size of legend.
          legend.spacing.y = unit(0.02, "cm")  # the distance of legends (y orientation).
      ) 

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.

## Warning: Removed 1709 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "Gammaproteobacteria_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 1709 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

Gammaproteobacteria with Ecosystem Subtype, Total Number of Bases, and Assembly type Outside Layer Label

ggtree(tree_Gammaproteobacteria, layout="circular", branch.length="none") %<+% 
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) + 
  new_scale_fill() + 
  geom_fruit(
      data=NEON_MAGs_metagenomes_chemistry_noblank,
      geom=geom_tile,
      mapping=aes(y=label, x=1, fill= AssemblyType),
      offset=0.08,   # The distance between external layers, default is 0.03 times of x range of tree.
      pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
      ) + 
  new_scale_fill() +
  geom_fruit(
          data=NEON_MAGs_metagenomes_chemistry_noblank,
          geom=geom_col,
          mapping=aes(y=label, x=TotalNumberofBases),  
          pwidth=0.4,
          axis.params=list(
                          axis="x", # add axis text of the layer.
                          text.angle=-45, # the text size of axis.
                          hjust=0  # adjust the horizontal position of text of axis.
                      ),
          grid.params=list() # add the grid line of the external bar plot.
      ) + 
      theme(#legend.position=c(0.96, 0.5), # the position of legend.
          legend.background=element_rect(fill=NA), # the background of legend.
          legend.title=element_text(size=7), # the title size of legend.
          legend.text=element_text(size=6), # the text size of legend.
          legend.spacing.y = unit(0.02, "cm")  # the distance of legends (y orientation).
      ) 

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "Gammaproteobacteria_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

Toolik Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry +
  geom_point(mapping=aes(color=Phylum))

ggsave(
  "NEON_MAGS_Toolik_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik Gammaproteobacteria Highlight Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular") +
    geom_hilight(node=259, fill="steelblue", alpha=.6)

ggsave(
  "Toolik_Gammaproteobacteria_Highlight_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik Gammaproteobacteria Highlight with Label Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") +
    geom_hilight(node=258, fill="grey", alpha=.6) +
    geom_cladelab(node=258, label="Pseudomonadota", align=TRUE, angle='auto', 
                  offset.text=0.5 , textcolor='black', barcolor='grey',barsize=1.5, fontsize=5)+
    geom_hilight(node=259, fill="steelblue", alpha=.6) +
    geom_cladelab(node=259, label="Gammaproteobacteria", align=TRUE, angle='auto', offset=0.75,  
                  offset.text=0.5 , textcolor='black', barcolor='steelblue',barsize=1.5, fontsize=5)

ggsave(
  "Toolik_Gammaproteobacteria_Highlight_with_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 14 in image

Toolik Gammaproteobacteria Label Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") %>% 
  collapse(node=259) + 
  geom_point2(aes(subset=(node==259)), shape=23, size=5, fill='steelblue') +  
  geom_cladelab(node=259, label="Gammaproteobacteria", align=TRUE,  
                  offset = 2, textcolor='steelblue')

ggsave(
  "Toolik_Gammaproteobacteria_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik Gammaproteobacteria Minimized Circular Tree

p <- ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none")
scaleClade(p, 259, .2) %>% collapse(259, 'min', fill="steelblue")  +
  geom_cladelab(node=259, label="Gammaproteobacteria", align=TRUE,  
                  offset = 0.2, textcolor='steelblue')

ggsave(
  "Toolik_MAGS_Gammaproteobacteria_Minimized_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik MAGS with Order Labels Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  geom_point(mapping=aes(color=Order))

ggsave(
  "Toolik_MAGS__with_Order_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik with Order and Assembly Type Labels Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  geom_point(mapping=aes(color=Order, shape = `Assembly Type`)) 

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point()`).

ggsave(
  "Toolik_MAGS_with_Order_and_Assembly_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point()`).

Toolik with Ecosystem Subtype System Rectangular Tree

ggtree(tree_bac_TOOL_MAGs)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tiplab(size=2, hjust=-.1) +
  geom_point(mapping=aes(color=`Ecosystem Subtype`))

ggsave(
  "Toolik_MAGS_with_Ecosystem_Subtype_System_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik with Bin Completeness Label Rectangular Tree

ggtree(tree_bac_TOOL_MAGs)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Bin Completeness`)) + 
  scale_colour_gradient(low='blue', high='red') +
  geom_tiplab(size=2, hjust=-.1) 

ggsave(
  "Toolik_MAGS_with_Bin_Completeness_Label_Rectangular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik with Ecosystem Subtype and Total number of Bases Label Circular Tree

ggtree(tree_bac_TOOL_MAGs, layout="circular")  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`))

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "Toolik_MAGS_with_Ecosystem_Subtype_and_Total_Number_of_Bases_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

Toolik triplot with Bin Completeness and Bin Contamination

ggtree(tree_bac_TOOL_MAGs)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Ecosystem Subtype`)) + 

# For unknown reasons the following does not like blank spaces in the names
  geom_facet(panel = "Bin Completeness", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point, 
      mapping=aes(x = BinCompleteness)) +
  geom_facet(panel = "Bin Contamination", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col, 
                aes(x = BinContamination), orientation = 'y', width = .6) +
  theme_tree2(legend.position=c(.1, .7))

ggsave(
  "Toolik_MAGS_triplot_with_Bin_Completeness_and_Bin_Contamination.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik triplot with Gene and GC Content

ggtree(tree_bac_TOOL_MAGs)  %<+%
  NEON_MAGs_metagenomes_chemistry + 
  geom_tippoint(aes(colour=`Ecosystem Subtype`)) + 

# For unknown reasons the following does not like blank spaces in the names
  geom_facet(panel = "Gene Count", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point, 
      mapping=aes(x = GeneCount))+
  geom_facet(panel = "% GC Content ", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col, 
                aes(x = GCassembled), orientation = 'y', width = .6) +
  theme_tree2(legend.position=c(.1, .7))

ggsave(
  "Toolik_MAGS_triplot_with_ Gene_and_GC_Content.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

Toolik with Ecosystem Subtype and Total Number of Bases in Outside Labels

ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") %<+% 
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) + 
  new_scale_fill() + 
  geom_fruit(
      data=NEON_MAGs_metagenomes_chemistry_noblank,
      geom=geom_tile,
      mapping=aes(y=label, x=1, fill= AssemblyType),
      offset=0.08,   # The distance between external layers, default is 0.03 times of x range of tree.
      pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
      )

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "Toolik_MAGS_with_Ecosystem_Subtype_and_Total_Number_of_Bases_in_Outside_Label_Circular_Tree.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

NEON with Ecosystem Subtype, Total Number of Bases, and Assembly type Outside Layer Label

ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") %<+% 
  NEON_MAGs_metagenomes_chemistry + 
  geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) + 
  new_scale_fill() + 
  geom_fruit(
      data=NEON_MAGs_metagenomes_chemistry_noblank,
      geom=geom_tile,
      mapping=aes(y=label, x=1, fill= AssemblyType),
      offset=0.08,   # The distance between external layers, default is 0.03 times of x range of tree.
      pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
      ) + 
  new_scale_fill() +
  geom_fruit(
          data=NEON_MAGs_metagenomes_chemistry_noblank,
          geom=geom_col,
          mapping=aes(y=label, x=TotalNumberofBases),  
          pwidth=0.4,
          axis.params=list(
                          axis="x", # add axis text of the layer.
                          text.angle=-45, # the text size of axis.
                          hjust=0  # adjust the horizontal position of text of axis.
                      ),
          grid.params=list() # add the grid line of the external bar plot.
      ) + 
      theme(#legend.position=c(0.96, 0.5), # the position of legend.
          legend.background=element_rect(fill=NA), # the background of legend.
          legend.title=element_text(size=7), # the title size of legend.
          legend.text=element_text(size=6), # the text size of legend.
          legend.spacing.y = unit(0.02, "cm")  # the distance of legends (y orientation).
      ) 

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.

## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size  * assembled, Gene Count  * assembled, Scaffold Count  * assembled, Genome MetaBAT Bin Count  * assembled, Genome EukCC Bin Count  * assembled, CRISPR Count  * assembled, GC Count  * assembled, GC  * assembled, Coding Base Count  * assembled, Coding Base Count %  * assembled, CDS Count  * assembled, CDS %  * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
  "Toolik_MAGS_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
  plot = last_plot(),
  device = NULL,
  path = "/cloud/project/images/Plots/Lab16",
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
)

## Saving 12 x 12 in image

## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).